The national secretary of the Health Services Union (HSU) claims Workplace Relations Minister Bill Shorten has been secretly working to undermine her.

Mr Shorten moved on Thursday to shut down the HSU's East branch, applying to have it taken over by an administrator "until democratic control of the union's east branch can be restored".

The application, when it is heard next week, will apply to the East branch and its 50,000 members in NSW and Victoria.

Elected officials would be cleaned out and national secretary Kathy Jackson would lose her high-paying job, as would general secretary Michael Williamson.

But Ms Jackson has come out fighting, calling Mr Shorten's move a cheap political stunt and accusing him of interfering in union affairs.

"For the minister to come in here and make out that he's got clean hands when his hands are dirty as, is just astounding," she said.

Where were they eight months ago when I raised these allegations? People in the ALP knew about this and did nothing about this.

HSU national secretary Kathy Jackson

"Where were they eight months ago when I raised these allegations? People in the ALP knew about this and did nothing about this. And here they are turning up today trying to make out that they're here to help.

"It would mean that the control of the union is taken out of the hands of the council. I'm not saying I disagree with that, what I'm disagreeing with is the manner that he's gone about it, coming in on his white horse to make out that he's here to help the HSU when it's only about helping Bill Shorten shore up his numbers."

Ms Jackson claims in a union document that both Mr Shorten and Senator Stephen Conroy tried to rally opposition against her. Both ministers deny any involvement.

"That's completely untrue. What I am interested in is to make sure that the members of this union actually have an accountable and effective union working in their interests," he said.

"I think in a lot of the debate and controversy in the last number of months there hasn't been a sufficient discussion about the members having their say.

"For the Government today to seek to intervene to pursue an application for an administrator is a grave and serious step. We do so because we believe that the legitimate interests of hospital workers in the health system need to come back to the fore.

"We have signalled today our intention to seek an administrator be appointed in the HSU East branch, which is the epicentre of lot of the problems which seem to be occurring. We've done this because we want to see the union return to the control of the members as soon as possible.

It's the members of the branch that stand to gain, because ultimately they're going to be in control of who's in the leadership positions. Who stands to lose? Well, Kathy Jackson and Michael Williamson stand to lose.

HSU acting president Chris Brown

"We've done this because there are 55,000 hospital cleaners, laundry attendants, catering staff and they - we can't continue this situation of day after day of counter-claim and allegation and counter-claim and allegation."